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Contents
require 'forwardable'
module SequenceServer
module BLAST
# Formatter is invoked during report generation or for results download to
# convert BLAST+ archive file to other formats. Formatter generates output
# in Job#dir. Output files persist till the job itself is deleted. Calling
# Formatter a second time (for the same input job and output format) will
# return saved ouput.
class Formatter
class << self
alias run new
end
extend Forwardable
def_delegators SequenceServer, :config, :sys
def initialize(job, type)
@job = job
@type = type
@format, @mime, @specifiers = OUTFMT[type]
run
end
attr_reader :format, :mime, :specifiers
def file
@file ||= File.join(job.dir, filename)
end
def filename
@filename ||= "sequenceserver-#{type}_report.#{mime}"
end
private
attr_reader :job, :type
def run
return if File.exist?(file)
command = "blast_formatter -archive '#{job.stdout}'" \
" -outfmt '#{format} #{specifiers}'"
sys(command, path: config[:bin], dir: DOTDIR, stdout: file)
rescue CommandFailed => e
# Mostly we will never get here: empty archive file,
# file permissions, broken BLAST binaries, etc. will
# have been caught before reaching here.
raise SystemError, e.stderr
end
end
end
end
# References
# ----------
# [1]: http://www.ncbi.nlm.nih.gov/books/NBK1763/
Version data entries
14 entries across 14 versions & 1 rubygems